Laboratoire d'Ingénierie des Fonctions Moléculaires | IFM

Marco CECCHINI
Maître de Conférences à l'Unistra

https://ifm.chimie.unistra.fr

Paola SAGER
email :paola.sager[at]unistra.fr
Phone : +33 (0)3 68 85 12 41

The Laboratoire d’Ingénierie des Fonctions Moléculaires is a modeling research team whose focus sits right at the interface between the domains of life science and material science. Our working approach is to start from problems of medical and/or technological relevance and develop computational strategies to provide an orthogonal and hopefully insightful view. Fundamental questions concerning with molecular self-assembly, the allosteric regulation of important neurotransmitter receptors, and the development of efficient numerical strategies to compute the free energy in solution are being tackled.

1. A. Bartocci, G. Pereira, M. Cecchini, E. Dumont, Capturing the Recognition Dynamics of para -Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. J. Chem. Inf. Model., acs.jcim.2c00483 (2022).
   
   
2. M. Scarpi-Luttenauer, et al., TiO4N2 complexes formed with 1,10-phenanthroline ligands containing a donor-acceptor hydrogen bond site: Synthesis, cytotoxicity and docking experiments. Inorganica Chim. Acta540, 121036 (2022).
   
   
3.  L. R. Kjølbye, et al., Towards design of drugs and delivery systems with the Martini coarse-grained model. QRB Discov., 1–51 (2022).
   
   
4. A. H. Cerdan, L. Peverini, J.-P. Changeux, P.-J. Corringer, M. Cecchini, Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway. Sci. Adv.8, eadc9340 (2022).
   
   
5. M. Cecchini, J.-P. Changeux, Nicotinic receptors: From protein allostery to computational neuropharmacology. Mol. Aspects Med.84, 101044 (2022).
   
   
6.  M. Sisquellas, M. Cecchini, PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening. Mol. Inform.40, 2100139 (2021).
   
   
7.  G. P. Pereira, M. Cecchini, Multibasin Quasi-Harmonic Approach for the Calculation of the Configurational Entropy of Small Molecules in Solution. J. Chem. Theory Comput.17, 1133–1142 (2021).
   
   
8. F. E. Blanc, M. Cecchini, An Asymmetric Mechanism in a Symmetric Molecular Machine. J. Phys. Chem. Lett.12, 3260–3265 (2021).
   
   
9. J. J. Montalvo‐Acosta, M. Dryzhakov, E. Richmond, M. Cecchini, J. Moran, A Supramolecular Model for the Co‐Catalytic Role of Nitro Compounds in Brønsted Acid Catalyzed Reactions. Chem. – Eur. J.26, 10976–10980 (2020).
   
   
10. A. H. Cerdan, M. Cecchini, On the Functional Annotation of Open-Channel Structures in the Glycine Receptor. Structure28, 690-693.e3 (2020).
    
    
11. A. H. Cerdan, et al., The Glycine Receptor Allosteric Ligands Library (GRALL). Bioinformatics36, 3379–3384 (2020).
    
    
12. S. J. Wodak, et al., Allostery in Its Many Disguises: From Theory to Applications. Structure27, 566–578 (2019).
    
    
13. X. Zeng, L. Zhu, X. Zheng, M. Cecchini, X. Huang, Harnessing complexity in molecular self-assembly using computer simulations. Phys. Chem. Chem. Phys.20, 6767–6776 (2018).
    
    
14. J. J. Montalvo-Acosta, P. Pacak, D. E. B. Gomes, M. Cecchini, A Linear Interaction Energy Model for Cavitand Host–Guest Binding Affinities. J. Phys. Chem. B122, 6810–6814 (2018).
15. S. Conti, M. Cecchini, Modeling the adsorption equilibrium of small-molecule gases on graphene: effect of the volume to surface ratio. Phys. Chem. Chem. Phys.20, 9770–9779 (2018).
    
    
16. A. H. Cerdan, N. É. Martin, M. Cecchini, An Ion-Permeable State of the Glycine Receptor Captured by Molecular Dynamics. Structure26, 1555-1562.e4 (2018).
    
    
17. F. Blanc, et al., An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics. Proc. Natl. Acad. Sci.115, 6213–6218 (2018).
    
    
18. N. E. Martin, S. Malik, N. Calimet, J.-P. Changeux, M. Cecchini, Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics. PLOS Comput. Biol.13, e1005784 (2017).
    
    
19. M. Harkat, et al., On the permeation of large organic cations through the pore of ATP-gated P2X receptors. Proc. Natl. Acad. Sci.114 (2017).
    
    
20. V. Ropars, et al., The myosin X motor is optimized for movement on actin bundles. Nat. Commun.7, 12456 (2016).
    
    
21. V. J. Planelles-Herrero, et al., Myosin MyTH4-FERM structures highlight important principles of convergent evolution. Proc. Natl. Acad. Sci.113 (2016).
    
    
22. J. J. Montalvo-Acosta, M. Cecchini, Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Mol. Inform.35, 555–567 (2016).
    
    
23.  F. Melaccio, et al., Space and Time Evolution of the Electrostatic Potential During the Activation of a Visual Pigment. J. Phys. Chem. Lett.7, 2563–2567 (2016).
    
    
24. C. Habermacher, et al., Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel. eLife5, e11050 (2016).
    
    
25. M. El Garah, et al., Atomically Precise Prediction of 2D Self-Assembly of Weakly Bonded Nanostructures: STM Insight into Concentration-Dependent Architectures. Small12, 343–350 (2016).
    
    
26. S. Conti, et al., Perchlorination of Coronene Enhances its Propensity for Self-Assembly on Graphene. ChemPhysChem17, 352–357 (2016).
    
    
27. S. Conti, M. Cecchini, Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach. Phys. Chem. Chem. Phys.18, 31480–31493 (2016).
    
    
28. M. Cecchini, J.-P. Changeux, The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation. Neuropharmacology96, 137–149 (2015).